Abstract
A number of methods based on time-dependent state space models have been proposed for inferring time-varying gene regulatory networks. These methods are capable of detecting a relatively small number of topological changes in gene regulatory networks. However, they are insufficient since there is a greater number of changes in the gene regulatory mechanisms; the function of a regulatory protein frequently changes due to post-translational modification, such as protein phosphorylation and ATP-binding. We propose a self-organizing state space approach to inferring consecutive changes in causalities between regulatory proteins from gene expression data. Hidden regulatory proteins are identified using a test-based method from genome-wide protein-DNA binding data. Application of this approach to cell cycle data demonstrated its effectiveness.
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Hirose, O., Shimizu, K. (2010). A Self-organizing State Space Approach to Inferring Time-Varying Causalities between Regulatory Proteins. In: Khuri, S., Lhotská, L., Pisanti, N. (eds) Information Technology in Bio- and Medical Informatics, ITBAM 2010. ITBAM 2010. Lecture Notes in Computer Science, vol 6266. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-15020-3_15
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DOI: https://doi.org/10.1007/978-3-642-15020-3_15
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